That kind of thing is done constantly throughout the process, every time two pieces of metal are assembled (and before they're assembled) they're checked for square and position.
If you're wondering about the parallelism of eg. linear guide rails, the install manuals for those rails typically have a guide for that.
Also, there are various techniques described in build threads here and in the CNC wood router section for determining parallelism.
I think most people skip it for the same reason they skip descriptions of installing a bolt... it's pretty basic for the most part. The best way to learn this stuff is to get a good book like "Machinery's Handbook" and read. Lots of great stuff in there.
If you have a specific question on the best way to measure a particular part of your machine while assembling to ensure it's parallel, then post and ask.
Taking a half step back, you might want to start with a solid wood cutting router table instead of a vertical mill. If you don't have enough experience with milling machines and machinist's skills to already have a bunch of different methods for checking parallel and square memorized, you're probably not going to be happy with the result you get when designing your own machine from scratch. There's a lot more to it than just arranging an X/Y table and Z quill of the size you want.
Maybe buy some plans from someone? Ever read the gingery books?